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An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels

The logistic mixed model (LMM) is well-suited for the genome-wide association study (GWAS) of binary agronomic traits because it can include fixed and random effects that account for spurious associations. The recent implementation of a computationally efficient model fitting and testing approach no...

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Autores principales: Shenstone, Esperanza, Cooper, Julian, Rice, Brian, Bohn, Martin, Jamann, Tiffany M., Lipka, Alexander E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6248992/
https://www.ncbi.nlm.nih.gov/pubmed/30462727
http://dx.doi.org/10.1371/journal.pone.0207752
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author Shenstone, Esperanza
Cooper, Julian
Rice, Brian
Bohn, Martin
Jamann, Tiffany M.
Lipka, Alexander E.
author_facet Shenstone, Esperanza
Cooper, Julian
Rice, Brian
Bohn, Martin
Jamann, Tiffany M.
Lipka, Alexander E.
author_sort Shenstone, Esperanza
collection PubMed
description The logistic mixed model (LMM) is well-suited for the genome-wide association study (GWAS) of binary agronomic traits because it can include fixed and random effects that account for spurious associations. The recent implementation of a computationally efficient model fitting and testing approach now makes it practical to use the LMM to search for markers associated with such binary traits on a genome-wide scale. Therefore, the purpose of this work was to assess the applicability of the LMM for GWAS in crop diversity panels. We dichotomized three publicly available quantitative traits in a maize diversity panel and two quantitative traits in a sorghum diversity panel, and them performed a GWAS using both the LMM and the unified mixed linear model (MLM) on these dichotomized traits. Our results suggest that the LMM is capable of identifying statistically significant marker-trait associations in the same genomic regions highlighted in previous studies, and this ability is consistent across both diversity panels. We also show how subpopulation structure in the maize diversity panel can underscore the LMM’s superior control for spurious associations compared to the unified MLM. These results suggest that the LMM is a viable model to use for the GWAS of binary traits in crop diversity panels and we therefore encourage its broader implementation in the agronomic research community.
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spelling pubmed-62489922018-12-06 An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels Shenstone, Esperanza Cooper, Julian Rice, Brian Bohn, Martin Jamann, Tiffany M. Lipka, Alexander E. PLoS One Research Article The logistic mixed model (LMM) is well-suited for the genome-wide association study (GWAS) of binary agronomic traits because it can include fixed and random effects that account for spurious associations. The recent implementation of a computationally efficient model fitting and testing approach now makes it practical to use the LMM to search for markers associated with such binary traits on a genome-wide scale. Therefore, the purpose of this work was to assess the applicability of the LMM for GWAS in crop diversity panels. We dichotomized three publicly available quantitative traits in a maize diversity panel and two quantitative traits in a sorghum diversity panel, and them performed a GWAS using both the LMM and the unified mixed linear model (MLM) on these dichotomized traits. Our results suggest that the LMM is capable of identifying statistically significant marker-trait associations in the same genomic regions highlighted in previous studies, and this ability is consistent across both diversity panels. We also show how subpopulation structure in the maize diversity panel can underscore the LMM’s superior control for spurious associations compared to the unified MLM. These results suggest that the LMM is a viable model to use for the GWAS of binary traits in crop diversity panels and we therefore encourage its broader implementation in the agronomic research community. Public Library of Science 2018-11-21 /pmc/articles/PMC6248992/ /pubmed/30462727 http://dx.doi.org/10.1371/journal.pone.0207752 Text en © 2018 Shenstone et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Shenstone, Esperanza
Cooper, Julian
Rice, Brian
Bohn, Martin
Jamann, Tiffany M.
Lipka, Alexander E.
An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels
title An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels
title_full An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels
title_fullStr An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels
title_full_unstemmed An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels
title_short An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels
title_sort assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6248992/
https://www.ncbi.nlm.nih.gov/pubmed/30462727
http://dx.doi.org/10.1371/journal.pone.0207752
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